title: Role of Su(Hw) in DNA amplification in Drosophila ovaries

city: Moscow

first: Nadezhda

last: Vorobyeva

address: Vavilova 34/5

country: Russia

institute: Institute of Gene Biology RAS

summary: Suppressor of Hairy wing (Su(Hw)) is an insulator protein that participates in regulating chromatin architecture and gene repression in Drosophila. In previous studies we have shown that Su(Hw) is also required for pre-replication complex (pre-RC) recruitment on Su(Hw)-bound sites (SBSs) in  Drosophila S2 cells and pupa. Here, we describe the effect of Su(Hw) on developmentally regulated amplification of 66D and 7F Drosophila amplicons in follicle cells (DAFCs), widely used as models in replication studies. We show Su(Hw) binding co-localizes with all known DAFCs in Drosophila ovaries, whereas disruption of Su(Hw) binding to 66D and 7F DAFCs causes a two-fold decrease in the amplification of these loci. The complete loss of Su(Hw) binding to chromatin violates pre-RC recruitment to all amplification regulatory regions of 66D and 7F loci at early oogenesis (prior to DAFCs amplification). These changes coincide with a considerable Su(Hw)-dependent condensation of chromatin at 66D and 7F loci. Although we observed the Brm, ISWI, Mi-2, and CHD1 chromatin remodelers at  SBSs genome wide, their remodeler activity does not appear to be responsible for chromatin decondensation at the 66D and 7F amplification regulatory regions. We have discovered that, in addition to the CBP/Nejire and Chameau histone acetyltransferases, the Gcn5 acetyltransferase binds to 66D and 7F DAFCs at SBSs and is dependent on Su(Hw). We propose that the main function of Su(Hw) in developmental amplification of 66D and 7F DAFCs is to establish a chromatin structure that is permissive to pre-RC recruitment.

overall_design: Ovaries were dissected from two developmental groups of females: 15 hours after eclosion (include egg chamber stages 1-8) and 32-34 hours after eclosion (include egg chamber 1-13).

first: N

first: M

middle: Y

last: Mazina


title: A dynamic transcriptome underling the light inhibition of mesocotyl elongation in rice seedling

status: Public on Aug 21 2021

city: Hangzhou

first: lv

middle: yu

last: song

address: CNRRI

country: China

institute: CNRRI

type: Expression profiling by high throughput sequencing

summary: The mesocotyl, a structure separating the grass seedling cotyledon from the coleoptile, exerts a major influence over the seedling’s ability to emerge. Its elongation is inhibited by light. A transcriptomic comparison between mesocotyl tissue which had developed in the dark and which had been exposed to light identified  a large number of differentially transcribed genes (DTGs)

overall_design: Six RNA pools were used to characterize the transcriptomic response of the mesocotyl to light: these were sampled from one to five days old seedlings grown in the dark (respectively, D_1d, D_3d, D_5d) and then from five day old dark-grown seedlings exposed to light for 30 min, 60 min or 24 h (L_0.5h, L_1h, L_24h).

first: Yusong

last: Lyu


title: ATAC chromatin accessibility profiling of terminal end buds and ducts from mouse mammary glands

status: Public on Aug 22 2021

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The mammary glands of adult female mice were divided into ductal tissue and terminal end buds (TEBs). Basal and luminal epithelial cells were FACS sorted and nuclei extracted for 75bp paired-end ATAC-seq profiling using an Illumina NextSeq 500 sequencer.

overall_design: Tissue was extracted from three independent mouse pools resulting in n=3 biological replicates for basal cells from from TEBs, luminal cells from ducts and luminal cells from TEBs and n=2 biological replicates for basal cells from ducts.

first: Michael

middle: J

last: Milevskiy

first: Jane

middle: E

last: Visvader


title: The elongation of the rice mesocotyl from darkness to light: an 'omics perspective.

type: Non-coding RNA profiling by high throughput sequencing

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Rapid production and genetic stability of human mesenchymal progenitor cells derived from human somatic cell nuclear transfer-derived pluripotent stem cells

status: Public on Aug 20 2021

city: Seongnam-si

first: Dong Ryul

last: Lee

state: Gyeonggi-do

address: 335, Pangyo-ro

country: South Korea

institute: CHA University

summary: Pluripotent stem cell-derived mesenchymal progenitor cells (PSC-MPCs) are primarily derived through two main methods: 3-dimensional (3D) embryonic body-platform (EB formation) and 2D direct differentiation method. We recently established somatic cell nuclear transfer (SCNT)-PSC lines and showed their stemness. In the present study, we produced SCNT-PSC-MPCs using a novel direct differentiation method, and the characteristics, gene expression, and genetic stability of these MPCs were compared with those derived through the EB formation method. The recovery and purification of SCNT-PSC-Direct-MPCs were significantly accelerated compared to those of the SCNT-PSC-EB-MPCs, but both types of MPCs expressed typical surface markers and exhibited similar proliferation and differentiation potentials. Additionally, the analysis of gene expression patterns using microarrays showed very similar patterns. Moreover, array CGH analysis showed that both SCNT-PSC-Direct-MPCs and SCNT-PSC-EB-MPCs exhibited no significant differences in copy number variation (CNV) or single-nucleotide polymorphism (SNP) frequency. These results indicate that SCNT-PSC-Direct-MPCs exhibited high genetic stability even after rapid differentiation into MPCs, and the rate at which directly derived MPCs reached a sufficient number was higher than that of MPCs derived through the EB method. Therefore, we suggest that the direct method of differentiating MPCs from SCNT-PSCs can improve the efficacy of SCNT-PSCs applied to allogeneic transplantation.

overall_design: Two human SCNT (somatic cell nuclear transfer)-PSC (pluripotent stem cell) lines (CHA-SCNT-hPSC-17 and hPSC-18) were differentiated into MPCs (mesenchymal progenitor cells) using the 3D embryonic body-platform (EB formation) method (CHA-SCNT-hPSC-17-EB-MPCs and CHA-SCNT-hPSC-18-EB-MPCs) and 2D direct method (CHA-SCNT-hPSC-17-Direct-MPCs and CHA-SCNT-hPSC-18-Direct-MPCs). We performed micro-array (GeneChip® Human Gene 2.0 ST Arrays) to compare the similarity of gene expression among isogenic MPCs according to differentiation method (CHA-SCNT-hPSC-17-EB-MPC vs Direct-MPC; CHA-SCNT-hPSC-18-EB-MPC vs Direct-MPC; duplicated).

first: Dong

middle: R

first: Soo

last: Jung

first: Jeoung


title: A Spatially-Defined Metastasis-Associated Microglia Subset Promotes Brain Metastasis Outgrowth through Cx3cr1-Mediated Interferon Response

city: South Bend

first: Qingfei

last: Wang

state: IN

address: 1234 N Notre Dame Ave, Harper Hall A121

department: Harper Cancer Research Institute

country: USA

institute: University of Notre Dame

summary: We use single cell RNA-seqencing (Drop-seq based) to profile and compare (1) the transcriptomes of naïve brain myeloid cells from wild type C57Bl/6 mice to brain metastasis-associated myeloid cells (Br.MAM) from C57Bl/6 mice bearing E0771 brain metastases and (2) the transcriptomes of Br.MAM in Cx3cr1+/- (het) mouse hosts bearing E0771 brain metastases to Br.MAM in Cx3cr1-/- (KO) mouse hosts bearing E0771 brain metastases.

overall_design: Naïve brains were obtained from 2-3 month old female C57Bl/6 mice without brain metastases. Brains bearing metastases initiated by cardiac injection of E0771 cells were obtained from 2-3 month old female mice (C57Bl/6; Cx3cr1+/-; Cx3cr1-/-) with established brain metastases (2-3 weeks post cardiac injection). Cell suspensions were prepared by percoll gradient centrifugation followed by MACS-based Cd11b enrichment to obtain suspensions enriched for myeloid cells.  Suspensions were run on Drop-seq platform and sequenced either on HiSeq or NextSeq sequencers.

first: Siyuan

last: Zhang

first: Ian

middle: H

last: Guldner


title: Transcriptomic analysis of several aneuploid strains from Angelika Amon lab

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

summary: The goal of the project was to study synthesis rates (SR) and mRNA levels (RA) genome wide in a series of aneuploid strains to check for the posible variation in SR and RA in the genes of the aneuploid chromosome withe regard to the rest of the genome. We used Genomic Run-On (GRO) experiment to mesaure SR and RA values.

overall_design: Cells were grown in YPD at 30ºC to 0.4-0.5 OD600 and cells were spun-down and collected. Note that each sample strain represents one replicate.

first: José

last: Pérez-Ortín

last: García-Martínez


title: A microRNAome sequencing of rice mesocotyl from darkness to light exposure

summary: Light exposure quickly inhibits the elongation of mesocotyl of rice seedling. The two corresponding periods from darkness to loght (D_5d, L_1h) were selected to perform small RNA sequencing.

overall_design: The microRNAome was directed to the two libraries which sampled from the mesocotyls of seedlings sowed in the dark for 5 days (D_5d), and then light exposure for 1 h (L_1h).


title: Integrated RNA-seq and ChIP-seq analysis reveals XBP1 as a regulator in Bisphenol A induced human uterine leiomyoma cell proliferation

city: haikou

first: Feng

middle: Tao

state: hainan

address: 58 Renmin Avenue, Meilan District

department: School of  Life and  Pharmaceutical Sciences

institute: Hainan University

summary:
Purpose:Our goal was to identify and characterize a new molecular target of Bisphenol A（BPA）in uterine leiomyoma cells to better understand how this compound may affect uterine leiomyomas growth and development.
Methods: Primary cultured cell lines of uterine leiomyoma were treated with 0.1% DMSO or 10.0 μmol/L BPA for 48 h before RNA-seq and histone 3 lysine 27 acetylation (H3K27ac) ChIP-seq were performed. Integrative analysis of ChIP-seq and RNA-seq data identifies the key transcription factor (TF)，target gene and signaling pathway. To confirm the expression level of TF and target gene in uterine leiomyomas tissues, we analyzed 10 human uterine leiomyoma tissues and the matched adjacent uterine smooth muscle tissues using western blotting, and 96 paired paraffin-embedded human uterine samples by immunohistochemistry(IHC). The ChIP assay used to confirm the combination between the TF and target gene. In order to verify the functions of key TF, lentivirus was used to knock down the expression level and detect the effects on cell proliferation, cell cycle, and cell tumorigenicity. We further conducted Western blot analysis to confirm the whether the downstream signaling pathway is activated.
RESULTS: Integrative Analysis of ChIP-seq and RNA-seq data identifies the key transcription factor XBP1and target gene ITGA2. The qPCR and ChIP- qPCR initially verified the sequencing results. XBP1 and ITGA2 were overexpressed in human uterine leiomyoma tissues. The IHC results confirmed that ITGA2 was significantly correlated with XBP1 expression (R = 0.6708, P < 0.001)， and the ChIP assay showed that XBP1 binds to the the ITGA2 predicted promoter region. BPA promoted uterine leiomyoma cells proliferation both in vitro and in vivo and that XBP1 expression levels modulated the cellular response to this endocrine disruptor. BPA upregulated ITGA2 through XBP1 and activated the downstream PI3K-AKT signaling pathway to promote the proliferation of human uterine leiomyoma cells.
CONCLUSION: In conclusion, our current work reveals a novel mechanism by which BPA promotes the proliferation in uterine leiomyoma cells. The XBP1 transcription factor regulates and activates the downstream ITGA2/PI3K/AKT pathway. By defining XBP1 as an important regulatory role of BPA in uterine leiomyoma cell proliferation, they provide new insights into the pathogenesis related to the exposure to BPA and other endocrine disruptors acting similarly, and XBP1 may serve as a candidate molecular target for intervention and treatment of uterine leiomyomas.

overall_design: Three representative primary cultured cell lines were selected, and cells were treated with 10.0 μmol/L BPA (Sigma) ,32.0 μmol/NP and 0.1% Dimethyl sulfoxide（DMSO，D2650, Sigma）for 48h before H3K27ac ChIP sequencing. For ChIP-Seq, 5ng of purified ChIP DNA were used to generate the sequencing library using a NEB kit and sequenced with the Illumina HiSeq X Ten. the cells treated with the 0.1% Dimethyl sulfoxide are the control group.

first: Zemin

last: Li

first: Yang

last: Shen


title: Oplopanax elatus Nakai chlorogenic-enriched fraction protective effect in APAP-induced liver injury

city: Yanji

first: xiaolong

last: jiang

address: #977, Gongyuan Road

institute: Yanbian university

summary:
Purpose: This study investigated the protective effect and further elucidated the mechanisms of action of O. elatus on acetaminophen (APAP)-induced liver injury (AILI).
Methods: O. elatus chlorogenic-enriched fraction (OEB) was administrated orally daily for seven consecutive days, followed by a single intraperitoneal injection of an overdose of APAP after the final OEB administration.
Results: OEB decreased alanine aminotransferase, aspartate aminotransferase, total cholesterol, total triglycerides contents, regulated superoxide dismutase, catalase, glutathione, malondialdehyde levels, and affected the metabolism of APAP. Furthermore, OEB treatment regulated lipid metabolism, activated the peroxisome proliferator-activated receptors signaling pathway in mice with AILI, affected immune cells, and decreased neutrophil infiltration.
Conclusions: This study indicated that OEB is a potential drug candidate for the prevention of APAP-induced hepatotoxicity and elucidated a potential protective mechanism by OEB.

overall_design: 6-8 weeks C57/B6 mice liver tissue of APAP group and OEB pre-treatment 7days group.

first: Zhe

last: Lian

first: Mei


title: A  degradome sequencing of rice mesocotyl from darkness to light exposure

first: lv

last: song

summary: Light exposure quickly inhibits the elongation of mesocotyl of rice seedling. The two corresponding periods from darkness to loght (D_5d, L_1h) were selected to perform degradome sequencing.

overall_design: The degradome was directed to the two libraries which sampled  from the mesocotyls of seedlings sowed in the dark for 5 days (D_5d), and then light exposure for 1 h (L_1h).

first: Yusong


title: Expression data of Panc1 cells treated with romidepsin and tamoxifen

city: Izumo

first: Yoshio

last: Honma

address: 89-1 Enya

department: Biochemistry

country: Japan

institute: Shimane University

summary: Tamoxifen enhances romidepsin-induced senescence in pancreatic cancer cells. We compared gene-expression profile among untreated control, romidepsin-treated, tamoxifen-treated, and romidepsin plus tamoxifen-treated Panc1 cells.

overall_design: Panc1 cells were treated with romidepsin and/or tamoxifen for 24 hours. Total RNA was extracted for hybridization on Affymetrix microarray. We compared gene-expression profile among untreated control, romidepsin-treated, tamoxifen-treated, and romidepsin plus tamoxifen.

first: Noriko

last: Ohkuni

first: Takeshi

last: Urano

first: Kenji

last: Tamura


title: Transcriptional profile changes in retinal pigment epithelial cell culture after treatment with an α7 nicotinic acetylcholine receptor agonist

city: Kalamazoo

first: Cindy

last: Linn

state: MI

address: 1903 W. Michigan Avenue

department: Biological Sciences

institute: Western Michigan University

summary:
Purpose: Eye drop application of PNU-282987, an α7 nAChR agonist, causes regeneration through development of Müller derived progeintor cells (MDPCs) that are generated as a result of signaling from activated retinal pigment epitheilal (RPE) cells . The goals of this study are to examine the transcrptional changes through RNA-seq after treatment with PNU-282987 in mammalian RPE cell culture that lead to the dedifferentation and generation of MDPCs in the adult mammalian retina. To validate the RNAseq findings, RT-qPCR was used. Finally, several genes that were identified were knocked out in RPE culture through a novel CRISPR/Cas12 system and the resulting activated supernatant was assayed for it's ability to cause neurogensis in the adult rodent retina.
Methods: Retinal pigment epithelium (RPE-J) cells were treated with DMSO (vehicle control), nicotine (an α7 nAChR agonist that does not cause regeneration as a control), or PNU-282987, or MLA (an α7 nAChR antagonist as a control). The cells were treated for either 30 minutes, 1 hour, 3 hours, 8 hours, or 12 hours. RNA was extracted from RPE-J cells using Zymo Direct-zol RNA miniprep kit and mRNA proflies were generated by GeneWiz with the Illumina NextSeq 550 high-output platform.
Results: Using an optimized data analysis workflow, GeneWiz mapped about 30 million sequence reads per sample to the rat genome (Rnor6.0) and identified over 15,000 transcripts. Deseq2 analysis was performed to determine log 2 fold changes in gene expression compared to DMSO control, nicotine control, and MLA control, and found over 450 significantly differentially expressed genes.  Twelve genes were validated with qRT–PCR to compare trends and were found to be consistent. Eight genes identified through RNA-seq involved in inflammation response, receptor signaling, WNT signaling and early retinal development were knocked out using CRISPR/Cas12 in RPE-J culture. Intravitreal injections of KO lines supernatant after treatment with PNU-282987 was assayed for invovlment of these genes in the adult neuroregeneration response.
Conclusions: PNU-282987 activation of RPE causes signficant transcript profile changes in RPE-J cell culture that leads to significant differentially expressed genes as seen in RNA-seq profiles and validated with qRT-PCR. Further, several genes identified in the RNA-seq were found to be necessary for the neurogenic response as seen with generation of KO lines of RPE.  Our study is the first to show that activaiton of the α7 nAChR on RPE leads to genetic changes sufficient to induce adult mammalian neurogenesis in the rodent retina and that several novel genes are invovled in this pathway in mammals as compared to other vertebrate models of retinal regeneration.

overall_design: RPE-J cell lines were treated with DMSO (vehicle control), nicotine (positive receptor activation control), MLA (negative control) or PNU-282987 for 30 minutes, 1 hour, 3 hours, 8 hours, or 12 hours before collection. RPE-J cells were trypsinized and collected for RNA extraction. RNA was shipped overnight on dry ice to GeneWiz for RNA-seq analysis resulting in Log2 fold changes for differentially expressed genes.

first: Sarah

last: Webster

middle: L


title: circRNA expression in breast cancer and adjacent non-tumor breast tissues

city: Lanzhou

first: HongLei

last: Wang

state: Gansu

address: 1 Donggang West Road

department: Department of Galactophore

institute: The First Hospital of Lanzhou University

summary: Circular RNAs (circRNAs) are key regulators in the development and progression of human cancers. A human circRNA microarray analysis was performed to screen for abnormally expressed circRNAs in breast cancer tissue and circRNA-000911 was identified as a circRNA which was significantly downregulated in breast cancer cells. Mechanistic investigations suggested that the enhanced expression of circRNA-000911 suppressed cell proliferation, migration and invasion, and promoted the apoptosis of breast cancer cells. The overexpression of circRNA-000911 may provide a future direction which may aid in the development of a novel treatment strategy for breast cancer.

overall_design: A total of 5 pairs of breast cancer tissue samples and adjacent non-tumor tissue samples were obtained from five BC patients. The circRNA expression profiles were detected with microarray, and validated by RT-qPCR.

first: Yi

last: Xiao

first: Li

last: Wu

first: DaChang

last: Ma


title: Oligodendrocyte regulation during autoimmune neuroinflammation

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

country: Germany

institute: Uniklinikum Erlangen

summary: The present study had the purpose to analyze the transcriptional state of oligodendrocytes in an animal model of multiple scleroris resembling autoimmune neuroinflammation and compared with control mice treated with ovalbumin. The results revealed that oligodendrocytes from the EAE (experimental autoimmune encephalomyelitis) model upregulate genes that are involved in immune processes providing evidence that oligodendrocytes can develop an immune phenotype in particular neuroinflammatory conditions.

overall_design: Mice with c56Bl/6j background were imunized with MOG 35-55 peptide or ovalbumin and monitored until peak of disease. At maximum disease point the animals were euthanized and the oligodendrocytes were isolated using magnetic beads with O4 antibodies. RNAs of 6 EAE mice and 4 ovalbumin treated mice (OVA) were combined in 3 EAE pools (containing 2 EAE RNAs per pool), and three OVA samples/pools, so that two of the four OVA RNAs were combined in one pooled sample, the other two analyzed separately.

first: María

middle: N

last: Alvarado

first: Ralf

last: Linker

first: Philipp

last: Kirchner

first: Arif

middle: B

last: Ekici


title: single-cell RNA sequencing for enteroids treated with IL-17

city: Seoul

first: Sung Noh

last: Hong

state: South Korea

address: 81 Irwon-Ro, Gangnam-gu

department: Gastroenterolgy

institute: Samsung Medical Center

summary: To evaluate the intestinal epithelial responses induced by IL-17, single-cell RNA-sequencing (scRNA-seq) was performed on the human small intestinal organoids (enteroids) sample of treated  with and without 100 mg/ml IL-17

overall_design:
control : human enteroids without IL-17 treatment (n =1, which combined cells from 3 human enteroids) vs. case: human enteroids with 100 ng/ml IL-17 treatment (n =1, which combined cells from 3 human enteroids)

**Raw Data not provided due to patient privacy concerns**

first: Sung

first: Chansu

last: Lee


title: DNA polymerase zeta contributes to heterochromatin replication to prevent genome instability

city: Paris

first: Jean-Charles

last: Cadoret

address: 15 rue hélène Brion

country: France

institute: CNRS/ Université de Paris

summary: The DNA polymerase zeta (Polζ) plays a critical role in bypassing DNA damage. REV3L, the catalytic subunit of Polζ is also essential in mouse embryonic development and cell proliferation for reasons that remain incompletely understood. In this study, we reveal that REV3L protein interacts with heterochromatin components including repressive histone marks, and localizes in pericentromeric regions through direct interaction with HP1 dimer. We demonstrate that Polζ/REV3L ensures progression of replication forks through difficult-to-replicate pericentromeric heterochromatin, thereby preventing spontaneous DNA and chromosome break formation. We also find that Rev3l-deficient cells are compromised in the repair of heterochromatin-associated DSBs, eliciting deletions in late replicating regions. Lack of REV3L leads to further consequences that may be ascribed to heterochromatin replication-associated functions of Polζ, with a disruption of the temporal replication program at specific loci. This is correlated with changes in epigenetic landscape and transcriptional control of developmentally regulated genes. These results reveal a new function of Polζ in preventing chromosome instability during replication of heterochromatic regions.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Nascent-DNA from early S-phase versus nascent-DNA from late S-phase

first: Barbara

last: Ben Yamin

first: Sana

last: Ahmed-Seghir

first: Junya

last: Tomida

first: Emmanuelle

last: Despras

first: Caroline

last: Pouvelle

first: Andrey

last: Iurchenko

first: Jordane

last: Goulas

first: Raphael

last: Corre

first: Quentin

last: Delacour

first: Nathalie

last: Droin

first: Philippe

last: Dessen

first: Didier

last: Goidin

first: Sabine

middle: S

last: Lange

first: Maria

middle: T

last: Mitjavila-Garcia

first: Giuseppe

last: Baldacci

first: Sergey

last: Nikolaev

first: Jean

middle: C

first: Richard

middle: D

last: Woodand

first: Patricia

last: Kannouche


title: RNA sequencing for enteroids treated with different concentrations of IL-17 (0 ng/ml. 1 ng/ml, 10 ng/ml and 100 ng/ml)

first: Sung Noh

last: Hong

summary: To evaluate the intestinal epithelial responses induced by IL-17, bulk RNA-sequencing (RNA-seq) was performed on the human small intestinal organoids (enteroids, n = 3) treated  with different concentrations of IL-17 (0 ng/ml. 1 ng/ml, 10 ng/ml and 100 ng/ml) .

overall_design:
enteroid without IL-17 treatment (n=3), enteroid with 1 ng/ml IL-17 treatment (n=3), enteroid with 10 ng/ml IL-17 treatment (n=3), and enteroid with 100 ng/ml IL-17 treatment (n=3),

**Raw Data not provided due to patient privacy concerns**

first: Sung

first: Chansu

last: Lee


title: Intestinal Akkermansia muciniphila predicts clinical response to PD1 blockade in advanced non-small cell lung cancer patients [RNA-seq].

city: Montréal

first: Bertrand

last: Routy

state: Quebec

address: 900 R. Saint-Denis

department: Axe Cancer

country: Canada

institute: CRCHUM

summary: The endpoint of this study was to prospectively validate the prognostic significance of fecal Akk in advanced NSCLC patients treated with first or second line ICI. We performed RNA sequencing to compare transcriptomic profiles of the different groups.

overall_design: Lung tumor mRNA profiles of 44 patients

first: Lisa

last: Derosa

first: Corentin

last: Richard

first: Laurence

last: Zitvogel


title: Differential Gene Expression Profiling of PBMCs in Crossbred and Tharparkar Cows in Relation to Lameness

city: Bareilly

first: Gyanendra

middle: Kumar

last: Gaur

state: UP

address: Izatnagar

department: LPM

country: India

institute: Indian Veterinary Research Institute

summary: Using Microarray technology, our aim is to identify diffrentially expressed genes for understanding different signalling pathways that leads to the lameness

overall_design: PBMCs were collected from Lame Crossbred, Normal Crossbred and Normal Tharparkar to identify DEGs

first: A

last: Baranwal

first: G

first: R

last: Gandham

first: M

last: Mukesh

first: S

last: Mahajan

last: Praharaj

last: Khan


title: Quantitative Analysis of Wild Type worms and vit-5 RNAi worms Transcriptomes

city: kunming

first: Yi-Cheng

last: Ma

email: 290361200@qq.com, mayc@ynu.edu.cn

state: yunnan

address: NO.2 North Cuihu Road

institute: Yunnan University

summary: Purpose: To identify the mechanism underlying reduced vitellogenin accumulation regulates the reproductive span, we used RNA-Seq analysis to study the transcriptional profiles Wild Type worms and vit-5 RNAi worms.

first: Jie

last: Tang

first: Cheng-Gang

last: zou

first: Ke-Qin

last: Zhang


title: Adaptive evolution under modest thermal stress improves the thermotolerance and ethanol fermentability of Saccharomyces cerevisiae

city: Changzhou

first: Xia

last: Yi

address: 21 Gehu Middle Road

institute: Changzhou University

summary: Thermotolerance development of robust Saccharomyces cerevisiae is necessary to enhance enzyme activity of cellulase, lower cooling costs, and reduce cell harm from the bad-distributed heat transfer in large-scale fermentation. The process-based studies of adaptive evolution have been well documented, but it remains unknown for the underlying molecular mechanism of the improved thermotolerance and the facilitated ethanol fermentability derived from adaptive evolution. Here, a robust thermotolerant S. cerevisiae Z100 was obtained with significantly improved ethanol fermentability under the stress of high temperature (50 oC) after 91 days’ adaptive evolution. RNA sequencing showed that adaptive evolution and its derived thermotolerance contributed to the unique gene transcriptional landscapes of the evolved strain. An interesting phenomenon was that the gene transcriptional signals of carbon metabolism were strengthened not at 50 oC but at 30 oC in S. cerevisiae Z100, and thus suggested that the improved thermotolerance led to the enhanced ethanol fermentability at 30 oC. The deeply repressed gene transcriptional expression indicated ribosome would be another key thermotolerant mechanism for the evolved strain. This study would provide a robust thermotolerant S. cerevisiae for bioethanol production and an important clue for future synthetic biology to thermotolerance engineering of fermentation strains.

overall_design: To find out genetic changes in the evolved S. cerevisiae Z100

last: Bao

first: Zhao

last: Yan


title: Chromatin accessibility landscape of freshly-isolated human and murine muscle satellite cells and myoblasts

city: Minneapolis

first: Alessandro

last: Magli

state: MN

address: 2231 6th St SE

department: Medicine

institute: University of Minnesota

summary: Muscle stem cells, also known as satellite cells, represent the main myogenic population accounting for skeletal muscle homeostasis and regeneration. Here, using the Assay for Transposase Accessible Chromatin followed by sequencing (ATAC-seq), we investigated the epigenetic landscape of activated human and murine satellite cells. Our analysis identified a compendium of putative regulatory elements defining activated satellite cells and myoblasts, respectively.

overall_design: Human and murine satellite cells were isolated from skeletal muscle tissue and processed for ATAC-seq. One fraction of the purified cells was cultured in vitro and the resulting proliferating myoblasts were processed for ATAC-seq analysis. These datasets were then compared to identify loci specific for each time point (fresh vs cultured) as well as loci conserved between human and murine cells.


title: RNA seq data of B cells from naïve, OPN knockout (Spp1-/-), ONKOSCID (SCID Spp1-/-) BALB/c mice

city: Durham

first: Nupur

last: Aggarwal

state: North Carolina

address: Jones building, Research drive

department: Immunology

institute: Duke University Medical School

summary: Marginal zone (IgM[hi] CD23[lo]MZ) and Follicular B (IgM[lo] CD23[hi]FB) cells in SCID Spp1-/- mice have different profile from naïve and Spp1-/- B cells. In addition, OPN mutation on the SCID background induced upregulation of genes involved in DNA replication and class switching of B cells

overall_design: Different B cell populations were FACS sorted from the spleen

first: Mari

last: Shinohara

first: Masashi

last: Kanayama


title: Allergens Elicit an Antiviral Signature in Dendritic Cells

city: Orlando

first: Justine

middle: T.

last: Tigno-Aranjuez

state: FL

address: 6900 Lake Nona Blvd., BSBS Bldg, Rm 370

department: BSBS, Immunity and Pathogenesis Division

institute: University of Central Florida

summary: This study compares the transcriptomic changes induced by three distinct aeroallergens in a dendritic cell line with the goal of finding similarities in the response at the gene expression level. Using RNA sequencing of DC2.4 cells, we find that house dust mite, cat hair and timothy grass allergen extracts all induce what appears to be an antiviral genetic signature despite the lack of any viral components in each allergen. Such information may be useful in trying to design therapeutics or interventions for allergic responses which could be effective for multiple allergens despite differences in source and structure.

overall_design: The murine dendritic cell line DC2.4 was left untreated or treated with house dust mite, cat hair or timothy grass allergen extracts prior to isolation of RNA for RNA sequencing. Two independent samples for each condition were analyzed.

first: Laurie

middle: M

last: Agosto

first: Haiyan

last: Hu


title: The specific interactions of Bcl9/Bcl9L with b-catenin and Pygopus promote breast cancer growth, invasion and metastasis

city: Basel

first: Ravi Kiran Reddy

last: KALATHUR

state: Basel

address: Mattenstrasse 28

department: Departement Biomedizin

country: Switzerland

institute: University of Basel

summary: Summary: We studied how the binding of beta-catenin to the transcriptional coactivators B-cell CLL/lymphoma 9 (Bcl9) and Bcl9-Like (Bcl9L) affected mammary gland carcinogenesis in the MMTV-PyMT transgenic mouse model of metastatic breast cancer. Conditional knockout of both Bcl9 and Bcl9L resulted into tumor cell death. In contrast, disrupting the interaction of Bcl9/Bcl9L with beta-catenin, either by deletion of their HD2 domains or by a point mutation in the N-terminal domain of beta-catenin (D164A), diminished primary tumor growth and tumor cell proliferation and reduced tumor cell invasion and lung metastasis. In comparison, the effect of disrupting the HD1 domain-mediated binding of Bcl9/Bcl9L to Pygopus was more moderate. Interfering with the beta-catenin - Bcl9/Bcl9L - Pygo chain of adaptors only partially impaired the transcriptional response of mammary tumor cells to Wnt3a and TGF-beta treatment. The results indicate that Bcl9/Bcl9L critically enforce canonical Wnt signaling in its contribution to breast cancer growth and malignant progression.

overall_design: RNA-Seq of tumor-derived primary epithelial cells with "B9/B9L deltaHD1/fl", "B9/B9L deltaHD1/-", "B9/B9L deltaHD2/fl" and "B9/B9L deltaHD2/-" genotypes treated with no, Wnt3a (3 days, 100ng/ml) or TGF-beta (4 days, 2ng/ml). RNA-Seq is performed in biological duplicates. rec = recombinant used for "B9/B9L deltaHD1/-" and "B9/B9L deltaHD2/-" genotypes.

first: Vida

last: Vafaizadeh

first: Ravi

middle: K

last: Kalathur

first: Gerhard

last: Christofori


title: Dlx1/2-Dependent Expression of Meis2 Promotes Neuronal Fate Determination in the Mammalian Striatum

status: Public on Aug 19 2021

city: Shanghai

first: Zihao

last: Su

address: 138 Yi Xue Yuan Road

institute: Fudan University

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Genome-wide loss of lineage fidelity is a hallmark of aging breast epithelia and reflects a biology convergent with susceptibility to cancer initiation

city: Duarte

first: Rosalyn

middle: W.

last: Sayaman

state: CA

address: 1500 E Duarte Rd

department: Population Sciences, Beckman Research Institute

institute: City of Hope Comprehensive Cancer Center

summary:
Purpose: Leveraging genome-wide lineage-specific transcriptional profiling of human mammary luminal epithelial cells (LEPs) and myoepithelial cells (MEPs) to elucidate the molecular mechanisms underlying aging-associated breast cancer susceptibility.
Methods: Human mammary luminal epithelial and myoepithelial cells were isolated from finite lifespan, non-immortalized human mammary epithelial cells (HMECs) derived from primary breast tissue of women across different age cohorts and breast cancer risk profiles. Transcriptional profiles of LEP and MEP cells were generated via RNA-sequencing performed on Illumina HiSeq 2500. RNA-Seq reads were trimmed using Trimmomatic software, and the processed reads were mapped back to the human genome (hg19) using TOPHAT2. Count matrices were generated using HTSeq.
Results: Genome-wide loss of lineage fidelity is a hallmark of aging breast epithelia. Age-dependent differential expression occurred almost exclusively in luminal cells characterized by luminal epithelial cells of older women expressing markers normally expressed in myoepithelial cells.  Luminal epithelial cells from histologically normal breast tissue from  younger women  who carry germline mutations in BRCA1, BRCA2, or PALB2 genes and who are considered to be clinically high risk for breast cancer also exhibited these hallmarks of accelerated aging. Furthermore, accelerated aging of these genetically high risk luminal epithelial cells could be predicted using a biological clock trained on gene expression and DNA methylation profiles of the luminal-specific ELF5 transcription factor.
Conclusions: Our study shows that lineage-specific analysis is critical to understanding the molecular mechanisms underlying aging-associated cancer susceptibility. Our results suggest that loss of lineage fidelity is a general manifestation of epithelia that are susceptible to cancer initiation. Moreover, breast aging hallmarks identified in our study reflect a convergent biology of cancer susceptibility, regardless of the specific underlying genetic or age-dependent risk.

overall_design: Luminal epithelial (LEPs) and myoepithelial (MEPs) cells enriched from finite lifespan, non-immortalized human mammary epithelial cells (HMECs) serve as our experimental model system. HMECs are derived from organoids isolated from collected breast tissue samples and grown to 4th passage [LaBarge et al., 2013, Garbe et al., 2009]. We examined genome-wide transcription in 108 enriched LEP and MEP samples from 46 women across a wide spectrum of ages and cancer risk profiles. We examined two age cohorts who were considered to have average risk for breast cancer: young ≤30y women considered to be premenopausal (age range 16-29y, n=32 LEP and MEP samples, m=11 subjects) and older ≥55y women considered to be postmenopausal (age range 56-72y, n=22 LEP and MEP samples, m=8 subjects). Samples from middle-aged women >30y <55y (n=6 LEP and MEP samples, m=3 subjects) were also included. Breast tissue samples from these subjects were collected from reduction mammoplasties (RM). We also examined women considered to be at higher risk to develop breast cancer based on accepted genetic or clinical risk factors (age range 25-72y, n=48 LEP and MEP samples, m=24 subjects). These women are either known carriers of high risk germline mutations (BRCA1, BRCA2, PALB2, PALB2/APC), and/or have personal history and/or known family history of breast cancer. Breast tissue samples from these subjects were collected from prophylactic mastectomies (PM) and normal contralateral-to-tumor (CLTT) or normal peripheral-to-tumor (PTT) tissue samples. Expression data from 4th passage HMEC were validated in primary organoids from young ≤30y and older ≥55y women with average risk for breast cancer (age range 16-66y, n=12 LEP and MEP samples, m=7 subjects.

middle: W

first: Masaru

last: Miyano

first: Sundus

middle: F

last: Shalabi

first: Michael

last: Todhunter

first: Martha

last: Stampfer

first: Mark

middle: A

last: LaBarge


title: RNA-seq and m6A-seq of Min6 cells were transfected with the GR cDNA expression vector or control vector

city: Nanjing

first: shao

middle: yi

last: xue

address: LongMian street

institute: Nanjing Medical University


title: Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation

city: Ann Arbor

first: Rachel

middle: Orion

last: Niederer

address: 1150 W. Medical Center Dr

department: Biological Chemistry

institute: University of Michigan

summary: Translational control shapes the proteome in normal and pathophysiological conditions. Current high-throughput approaches reveal large differences in mRNA-specific translation activity but cannot identify the causative mRNA features. We developed direct analysis of ribosome targeting (DART) and used it to dissect regulatory elements within 5′ untranslated regions that confer thousand-fold differences in ribosome recruitment in biochemically accessible cell lysates. Using DART, we identified novel translational enhancers and silencers, determined a functional role for most alternative 5′ UTR isoforms expressed in yeast, and revealed a general mode of increased translation via direct binding to a core translation factor. DART enables systematic assessment of the translational regulatory potential of 5′ UTR variants, whether native or disease-associated, and will facilitate engineering of mRNAs for optimized protein production in various systems.

overall_design: RNA-seq of ribosome bound, unbound, and input fractions

middle: O

first: Maria

last: Rojas-Duran

first: Boris

last: Zinshteyn

first: Wendy

middle: V

last: Gilbert


title: RNA-seq of Min6 cells were transfected with the GR cDNA expression vector or control vector

summary: In order to investigated the underlying molecular mechanism of GR’s effects, we transfected the Min6 cell with the GR cDNA expression vector or control vector, and then extracted RNA of Min6 cells for RNA sequencing. We studied the gene-expression differences resulting in GR overexpress. A total of 21542 gene transcripts was captured,and 233 genes showed significant expression differences (p-value<0.05,|log2Foldchange|>1) between the two group. Further GO analysis and KEGG analysis found that GR overactivation instigates dysregulated autophagy in beta-cells

overall_design: mRNA of Min6 cells transfected Control vector or GR expression vector

first: Xiao

last: Han

first: Fang

last: Chen

first: Tijun

last: Wu

first: Yixue

last: Shao


title: m6A-seq of Min6 cells were transfected with the GR cDNA expression vector or control vector

summary: To further explore the underlying molecular mechanism of GR’s effects, we transfected the Min6 cell with the GR cDNA expression vector or control vector, and then extracted RNA of Min6 cells. M6A antibody was used to specifically recognize m6A on mRNA. methylation modified RNA fragments were obtained by immunoprecipitation and used for high-throughput sequencing. By comparing the captured RNA fragments, we found that there were 22381 difference peaks between GR overexpression group and control group, among which 3659 binding peaks were significantly different.Further analysis the MeRIP sequencing results of MIN6 cells overexpressing GR revealed that  decreased m6A was detected in a large number of autophagy-related mRNAs.

overall_design: Input and m6A-IP mRNA of Min6 cells transfected Control vector or GR expression vector


title: Genome-wide maps of histone modification H3K4me3 in Daudi cells.

city: Bunkyo-ku

first: Yasuhiro

last: Fujiwara

address: 1-1-1 Yayoi

department: IQB

institute: The University of Tokyo

summary: We report the updated method for CUT&Tag technology for high-throughput profiling of histone modifications or transcription factors in mammalian cells. By using using hand-made concanavalin A conjugated beads, we greatly improved handling and suspendability of cell-bound magentic beads and increased sensitivity for detecting peaks compared with conventional concanavalin A coated magnetic beads. This study provides a framework for the application of epigenome studies using mammalian cells.

overall_design: Examination of histone modification H3K4me3 in Daudi cells.

first: Yuki

last: Okada


title: Whole RNA sequencing data

city: Kobe

first: Masato

last: Komatsu

state: Hyogo

address: 7-5-2 Kusunoki-Cho, Chuo-Ku

department: Diagnostic Pathology

institute: Kobe University Hospital

summary: We report a single pulmonary tumor with EWSR1-CREM fusion

overall_design: Whole RNA sequencing data derived from a pulmonary tumor


title: Transcriptomes of MPO-deficient patients with generalized pustular psoriasis reveals expansion of CD4+ cytotoxic T cells and an involvement of the complement system

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

institute: Uniklinikum Erlangen

summary: We performed a systematic analysis of differential gene expression in a wide set of peripheral human immune cells of MPO-deficient patients using RNA-sequencing of neutrophils in stable disease state.

overall_design: Transcriptome Sequencing of neutrophils from 3 GPP patients and 4 healthy donors

first: Stefan

last: Haskamp

first: Ulrike

last: Hüffmeier


title: Transcriptomes of MPO-deficient patients with generalized pustular psoriasis reveals expansion of CD4+ cytotoxic T cells and an involvement of the complement system [PBMCs]

summary: We performed a systematic analysis of differential gene expression in a wide set of peripheral human immune cells of MPO-deficient patients using single cell RNA-sequencing (scRNAseq) of peripheral blood mononuclear cells (PBMCs) in stable disease state.

overall_design: single cell RNA-sequencing of peripheral blood mononuclear cells from 2 patients and 3 healthy donors, where samples from the first patient were extracted at two different time points


title: Circular RNA Expression Profiles during brown adipogenesis

city: Xinyang

first: pengpeng

last: Zhang

state: Henan

address: No.237 Nanhu Road Shihe District

institute: Xinayang Normal University

summary: The aims of the current study were to characterize theprofile of circRNA during BAT adipocytes adipogenesis.

overall_design: Primary BAT preadipocytes were isolated, and induced to adipogenic differentiation. The samples were collected on Day0, Day 4 and day 8 post differentiation

first: Pengpeng

first: Yongjie

last: Xu

first: Haixia

first: Cencen

last: Li


title: Spatiotemporal and functional heterogeneity of the hematopoietic stem cell-competent hemogenic endothelial cells in mouse embryos

city: Beijing

first: Gong

last: Yandong

address: DongDaJie #8

institute: the Fifth Medical Center of the PLA General Hospital

summary: Hematopoietic stem cells (HSCs) are derived from hemogenic endothelial cells (HECs) during embryogenesis. The HSC-primed HECs are peak at embryonic day (E) 10 and have been efficiently captured by the marker combination CD41-CD43-CD45-CD31+CD201+Kit+CD44+ (PK44) in the aorta-gonad-mesonephros (AGM) region of mouse embryos most recently. In the present study, we investigated the spatiotemporal and functional heterogeneity of PK44 cells around the time of emergence of HSCs. First, PK44 cells in E10 AGM region could be further divided into three molecularly different populations showing endothelial- or hematopoietic-biased characteristics. Specifically, with the combination of Kit, the expression of CD93 or CD146 could divide PK44 cells into endothelial- and hematopoietic-feature biased populations, which was further functionally validated at single cell level. Next, PK44 population could also be detected in the yolk sac, showing a developmental dynamics and functional diversification similar to those in the AGM region. Importantly, PK44 cells in the yolk sac demonstrated an unambiguous multi-lineage reconstitution capacity after in vitro incubation. Regardless of the functional similarity, PK44 cells in the yolk sac displayed transcriptional features different to those in the AGM region. Taken together, our work delineated the spatiotemporal characteristics of HECs represented by PK44, and revealed a previously unknown HSC competence of HECs in the yolk sac. These findings provided a fundamental basis for in-depth studying the different origins and molecular programs of HSC generation in the future.

overall_design: PK44 (CD41-CD43-CD45-CD31+CD201+Kit+CD44+) population have been identified as HSC-competent HECs in our precious study.With the aim of further exploring whether yolk sac PK44 cells can undergo EHT and have endothelial-hematopoietic dual potential like that in AGM region, we sorted and performed scRNA-seq.

first: Yunqiao

first: Yandong

last: Gong


title: Single-cell analysis reveals innate lymphoid cell lineage infidelity in atopic dermatitis

city: Vienna

first: Natalia

last: Alkon

address: Währinger Gürtel 18-20

department: Department of Dermatology

country: Austria

institute: Medical University of Vienna

summary:
Background: Although ample knowledge exists about phenotype and function of cutaneous T lymphocytes, much less is known about the lymphocytic components of the skin’s innate immune system.
Objective: To better understand the biologic role of cutaneous innate lymphoid cells (ILCs), we investigated their phenotypic and molecular features under physiologic (normal human skin [NHS]) and pathologic (lesional skin of patients with atopic dermatitis [AD]) conditions.
Methods: Skin punch biopsies and reduction sheets as well as blood specimens were obtained from either patients with AD or healthy individuals. Cell and/or tissue samples were analyzed by flow cytometry, immunohistochemistry, and single-cell RNA sequencing or subjected to in vitro / ex vivo culture.
Results: Notwithstanding substantial quantitative differences between NHS and AD skin, we found that the vast majority of cutaneous ILCs belong to the CRTH2+ subset and reside in the upper skin layers. Single-cell RNA sequencing of cutaneous ILC-enriched cell samples confirmed the predominance of biologically heterogeneous group 2 ILCs and, for the first time, demonstrated considerable ILC lineage infidelity (coexpression of genes typical of either type 2 [GATA3 and IL13] or type 3/17 [RORC, IL22, and IL26] immunity within individual cells) in lesional AD skin, and to a much lesser extent, in NHS. Similar events were demonstrated in ILCs from skin explant cultures and in vitro expanded ILCs from the peripheral blood.
Conclusion: These findings support the concept that instead of being a stable entity with well-defined components, the skin immune system consists of a network of highly flexible cellular players that are capable of adjusting their function to the needs and challenges of the environment.

overall_design:
Investigation of cutaneous ILCs in AD and NHS
NOTE FROM SUBMITTER: Due to patient privacy concerns raw data is not provided.

first: Wolfgang

last: Bauer

first: Thomas

last: Krausgruber

first: Issac

last: Goh

first: Johannes

last: Griss

first: Vy

last: Nguyen

first: Baerbel

last: Reininger

first: Christine

last: Bangert

first: Clement

last: Staud

first: Patrick

last: Brunner

first: Christoph

last: Bock

first: Muzlifah

last: Haniffa

first: Georg

last: Stingl


title: Dlx1/2-Dependent Expression of Meis2 Promotes Neuronal Fate Determination in the Mammalian Striatum [RNA-seq]

first: Zihao

last: Su

summary:
Purpose:To asses changes in gene expression profiles from the E14.5  littermate controls LGE and Meis2-CKO  mice.
Methods:The LGEs from E14.5 Meis2-CKO mutant and Control brains (n = 4 per group) were dissected, and RNA was isolated with the Direct-zol RNA Miniprep kit (Zymo, catalog #R2050) following the manufacturer’s instructions.
Results: Identified 161 genes with downregulated RNA expression and 94 genes with upregulated RNA expression

overall_design: LGE mRNA profiles of E14.5 old control (Ctrl) and Meis2-CKO mice

first: Zhuangzhi

last: Zhang


title: Phase 1 Study Combining Alisertib with Nab-Paclitaxel in Patients with Advanced Solid Malignancies (NCT01677559)

city: St. Louis

first: Kian-Huat

last: Lim

state: MO

address: 4566 Scott Avenue, Room 502

department: Internal Medicine/Oncology

institute: Washington University School of Medicine

summary: WES and RNAseq from tumor samples of patients treated on clinical trial

overall_design: Pretreatment biopsies were obtained from responders and non-responders

first: Andrea

last: Wang-Gillam


title: RNA-seq of skeletal muscle model for myotonic dystrophy type 1 (DM1)

city: Houston

last: Cooper

state: TX

address: One Baylor Plaza

department: Pathology & Immunology

institute: Baylor College of Medicine

summary: We have developed an inducible, skeletal muscle-specific mouse model of DM1 (CUG960) that expresses 960 CUG repeat-expressing animals (CUG960) in the context of human DMPK exons 11-15. CUG960 RNA-expressing mice induced at postnatal day 1, as well as adult-onset animals, show clear, measurable muscle wasting accompanied by severe histological defects including central myonuclei, reduced fiber cross-sectional area, increased percentage of oxidative myofibers, the presence of nuclear RNA foci that colocalize with Mbnl1 protein, and increased Celf1 protein in severely affected muscles. Importantly, muscle loss, histological abnormalities and RNA foci are reversible, demonstrating recovery upon removal of toxic RNA. RNA-seq and protein array analysis indicate that the balance between anabolic and catabolic pathways that normally regulate muscle mass may be disrupted by deregulation of platelet derived growth factor receptor beta signaling and the PI3K/AKT pathways, along with prolonged activation of AMP-activated protein kinase alpha signaling. Similar changes were detected in DM1 skeletal muscle compared with unaffected controls.

overall_design: RNA was isolated from gastrocnemius or quadriceps muscles. Animals were induced to express expanded CUG repeats using doxycycline (dox) or no dox controls at PN1 and tissues were collected at the indicated time points. The Genomic and RNA Profiling Core (GARP) at Baylor College of Medicine (BCM) performed HiSeq library preparation and Illumina sequencing of 100-bp paired-end reads on a HiSeq 2500 sequencer. RNA was poly-A selected, barcoded and run in eight lanes.

first: Ginny

middle: R

last: Morriss

first: Kimal

last: Rajapakshe

first: Shixia

last: Huang

first: Cristian

last: Coarfa


title: Alginate-based 3D culture of human induced pluripotent stem cells and their differentiation to functional dopaminergic neurons

city: Bozen/Bolzano

first: Christian

middle: X.

last: Weichenberger

state: BZ

address: Galvanistraße/via Galvani 31

department: Institute for Biomedicine

country: Italy

institute: EURAC Research

summary: Human induced pluripotent stem cells (hiPSCs) represent an unlimited cell source for the generation of in vitro models of patient-specific dopaminergic (DA) neurons, posing a possibility to overcome the restricted accessibility to disease-affected tissue for mechanistic studies on Parkinson’s disease (PD). However, the complexity of the human brain is not fully recapitulated by existing monolayer culture methods. Consequently, neurons differentiated in a three dimensional (3D) in vitro culture system might better mimic the in vivo cellular environment for basic mechanistic studies and represent better predictors of drug responses in vivo. Thus, in this work we established a new in vitro cell culture model based on the microencapsulation of hiPSCs in small alginate/fibronectin beads and their differentiation to DA neurons. Optimisation of hydrogel matrix concentrations and composition resulted in high viability of embedded iPSCs. Neural differentiation capacity and DA neuronal yield, analyzed by qRT-PCR, immunofluorescence, and western blot analyses, were increased in the 3D neuronal cultures compared to neurons generated using the conventional 2D culture system. Additionally, electrophysiological parameters and metabolic switching profile supported the increased functionality and an anticipated metabolic resetting of neurons grown in alginate scaffolds with respect to the 2D neurons. We also report long-term maintenance of neuronal cultures and mature functional properties. Furthermore, our findings indicate that our 3D model system can recapitulate mitochondrial superoxide production as an important mitochondrial phenotype observed in PD patients’-derived neurons and that this phenotype might be detectable earlier during neuronal differentiation. Taken together, these results indicate that our alginate-based 3D culture system offers an advantageous strategy for the reliable and rapid derivation of mature and functional DA neurons from iPSCs.

overall_design: mRNA profiles of 3D and 2D cultured hiPSCs differentiating to dopaminergic neurons at T0, day10, day20 and day35.

first: Valentina

last: Gilmozzi

first: Giovanna

last: Gentile

first: Diana

last: Riekschnitz

first: Michael

last: Von Troyer

first: Alexandros

last: Lavdas

first: Emanuela

last: Kerschbamer

middle: X

first: Marcelo

last: Rosato Siri

first: Simona

last: Casarosa

first: Luciano

last: Conti

first: Peter

middle: P

last: Pramstaller

first: Andrew

last: Hicks

first: Irene

last: Pichler

first: Alessandra

last: Zanon


title: Ilicicolin-A exert antitumor effect in CRPCa via suppressing EZH2 signaling pathway

city: guangzhou

first: zhang

middle: zhen

last: hua

state: guangdong

address: xiaoguwei

department: college of pharmacy

institute: Sun Yat-Sen University

summary: Enhancer of zeste homolog 2 (EZH2) has critical roles in prostate cancer (PCa) progression and drug-resistance, which remains an obstacle for PCa treatment. Enzalutamide (ENZ) is a second-generation androgen receptor (AR) antagonist employed for treatment of metastatic castration-resistant prostate cancer (mCRPCa). A considerable proportion of tumors eventually develop resistance during treatment. Thus, agents that can overcome resistance to PCa are needed urgently. Ilicicolinal A (Ili-A), an ascochlorin derivative isolated from the coral-derived fungus Acremonium sclerotigenum GXIMD 02501, shows activity in human PCa cells, but its mechanism of action against CRPCa is not known. Here, RNA-sequencing showed the EZH2 pathway to be involved in PCa proliferation. Ili-A at low doses inhibited the transcriptional activity of EZH2 and AR targets by changing their protein expression. Interestingly, Ili-A suppressed the binding of EZH2 to promoter regions in AR/serine/threonine polo-like kinase-1/aurora kinase A. Moreover, low-dose Ili-A showed a synergistic effect with enzalutamide to inhibit survival of CRPCa cells in vitro, and enhanced the anti-cancer effect of enzalutamide on CRPCa xenografts with minimal side-effects. These data suggest that Ili-A could be used in combination with enzalutamide to treat CRPCa.

overall_design: C4-2B cells were treated with vehicle or the small molecule IliA (5 μM) and IliA (10 μM), for 48 h before RNA extraction. RNA-seq libraries were from 1 μg total RNA which was extracted using the total RNA isolation kit (Tiangen, BJ, China) and reverse transcribed with reverse transcriptase M-MLV (Takara, DL, China), according to the manufacturer's instructions. Libraries were validated with an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

first: Lang

last: Guo

first: Xiaowei

last: Luo

first: Ping

last: Yang


title: The novel long noncoding RNA lncRNA-AU021063, induced by IL-6/Arid5a signaling, exacerbates breast cancer invasion and metastasis by stabilizing Trib3 and activating the Mek/Erk pathway

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Transcriptomic profiling for research of molecular mechanisms implicated in the differentation of Human Neural Stem Cells

city: Majadahonda

first: Victoria

last: López-Alonso

address: Crta Majadahonda Pozuelo km 2

department: Computational Biology

institute: Institute of Health Carlos III

summary: We conduct RNA sequencingof the human neural stem hNS1 as a in vitro model to profile gene expression alterations in differentiation versus proliferation and we analyzed the relevance of the deregulated genes and a review of signaling pathways and analogies with previous information obtained from neural databases

overall_design: Examination of human neural stem hNS1 as a in vitro model to profile gene expression alterations in differentiation versus proliferation

first: Isabel

last: Liste

first: Raquel

last: Coronel

first: Rosa

last: Gonzalez


title: The novel long noncoding RNA lncRNA-AU021063, induced by IL-6/Arid5a signaling, exacerbates breast cancer invasion and metastasis by stabilizing Trib3 and activating the Mek/Erk pathway (ncRNA-Seq)

summary: Interleukin (IL-6) is a pleotropic cytokine with both tumor-promoting and -inhibitory effects on breast cancer growth. However, the mechanisms governing the outcome of IL-6 on cancer progression remain to be clarified. Our study unraveled a novel long noncoding RNA (lncRNA)-AU021063 downstream of IL-6 signaling. We found that IL-6 induced the expression of lncRNA-AU021063 predominantly in breast cancer compared to other cancer types. Mechanistically, IL-6 induced AT-rich interactive domain 5a (Arid5a) expression, which promotes the transcription of lncRNA-AU021063. In turn, lncRNA-AU021063 promotes breast cancer metastasis through stabilizing tribbles homolog 3 (Trib3) and activating Mek/Erk signaling pathway. Genetic ablation of either Arid5a, lncRNA-AU021063 or Trib3 abolished breast cancer metastasis in vitro and in vivo. Overall, our study highlights the importance of IL-6-Arid5a-lncRNA-AU021063 axis in regulating breast cancer invasiveness and metastasis, which may provide potential novel therapeutics for breast cancer.

overall_design: To identify novel lncRNAs that may be involved in the pathogenesis of breast cancer associated with IL-6/Arid5a signaling, we performed next-generation RNA sequencing (lncRNA sequencing) in stimulated WT and Arid5a-/- MEFs with or without IL-6 treatment.

first: Kishan

last: Nyati

first: Tadamitsu

last: Kishimoto


title: RNA-seq of Solanum lycopersicum cv Micro-Tom (wild-type and 35S::AtCKX2) infected with the fungus Moniliophthora perniciosa

status: Public on Aug 24 2021

city: Piracicaba

first: Paulo

last: Teixeira

state: SP

address: Av. Pádua Dias, 11

department: Biology

country: Brazil

institute: University of São Paulo (ESALQ/USP)

summary: We report that Moniliophthora perniciosa biotype-S, which infects Solanaceae, manipulates the tomato Micro-Tom (MT) cytokinin (CK) metabolism. We evaluated the transcriptome of wild-type MT plants and of the transgenic line that overexpresses the Arabidopsis CYTOKININ OXIDASE-2 gene (35S::AtCKX2) inoculated or not with M. perniciosa at 12, 24, and 48 hours after inoculation (hai), and 5, 10, 20, and 30 days after inoculation (dai).

overall_design: Wild-type MT and the transgenic line 35S::AtCKX2 were germinated in a 1:1 mixture of substrate:expanded vermiculite and grown under controlled conditions in a growth chamber at 25oC, 14 h photophase and 80% humidity. The shoot apex and axillary buds of 17-d-old tomato seedlings were inoculated with 70 µL of 10^6 basidiospores in 0.3% agar-water (w/v), and the plants were kept in a humid chamber for 48 h. Control plants were treated with 0.3% agar-water. Five replicates of each treatment were collected at 12, 24, and 48 hai, and at 5, 10, 20, and 30 dai.

first: Juliana

last: Costa

first: Daniele

last: Paschoal

first: Antonio

last: Figueira


title: The novel long noncoding RNA lncRNA-AU021063, induced by IL-6/Arid5a signaling, exacerbates breast cancer invasion and metastasis by stabilizing Trib3 and activating the Mek/Erk pathway (ChIP-Seq)

overall_design: We examined the binding affinity of Arid5a to the lncRNA-AU021063 promoter region using ChIP-seq in stable HA-tagged Arid5a-overexpressing 4T1 cells with or without IL-6 stimulation.


title: VersicanV1 promotes proliferation and metastasis of hepatocellular carcinoma through the activation of EGFR-PI3K-AKT pathway

city: Shanghai

first: Guangyan

last: Zhangyuan

state: Shanghai

address: 197 Ruijin Er Road

department: Department of General Surgery, Pancreatic Disease Center

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

summary: Versican has been reported to participate in carcinogenesis in several malignant tumors. However, the accurate role of Versican in hepatocellular carcinoma (HCC) remains an enigma. Our current study reveals that VersicanV1, a predominant isoform of Versican in liver, is significantly unregulated in HCC tissues and correlates with poor prognosis. Both in vitro and in vivo experiments show that knockdown of VersicanV1 in HCC cells attenuates cancer cells malignancy. Further studies identify the positive role of VersicanV1 in aerobic glycolysis. Mechanistic investigation discovers the activation of EGFR-PI3K-AKT pathway in HCC cells expressing high VersicanV1. Moreover, EGF-like motif is indispensable for VersicanV1 to promote Warburg effect of HCC cells and subsequently, proliferation, invasion and metastasis ability via activation of EGFR-PI3K-AKT axis. Taken together, our research highlights a novel role of VersicanV1 in the progression of HCC, suggesting that VersicanV1 is an indicator for prognosis and a potential therapeutic target of HCC.

overall_design: Liver cancer cell line Huh7 was transfected with control and VersicanV1 knockdown lentivirus in triplicate. Cell lysis were subjected to RNA sequencing, using Illumina GAIIx

first: Wenjie

last: Zhang

first: Fei

last: Wang

first: WeiWei

last: Yu

first: Kangpeng

last: Jin

first: Yang

last: Liu

first: Haitian

first: Yin

last: Yin

first: Xuewen

last: Tao

first: Beicheng

last: Sun


title: NPAS4 regulates the transcriptional response of suprachiasmatic nucleus neurons to photic input

status: Public on Aug 23 2021

city: Dallas

first: Genevieve

last: Konopka

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

summary: In mammals, the hypothalamic suprachiasmatic nucleus (SCN) is the master circadian pacemaker. It is primarily entrained by environmental photic stimuli. However, the molecular bases of the response of heterogeneous cells in the SCN to photic stimuli is not fully understood. In this study, we combined bulk RNA/ChIP/single nuclei sequencing with circadian behavioral assays to investigate cellular identities in the SCN and explore how they react to photic stimuli. We identified 3 major peptidergic cells in the SCN, Avp-expressing, Vip-expressing and Cck-expressing cells. In each peptidergic cell type, there is a light responsive cell cluster, and each of these is enriched for Neuronal PAS Domain Protein 4 (NPAS4) target genes. In addition, Npas4 null mice have a 1hr longer circadian period in constant darkness and a damped phase responsive curve to photic stimuli. Bulk RNA seq in Npas4-/- SCN revealed a reduced magnitude of light induced gene expression. Together, our data indicate that NPAS4 is part of the machinery that orchestrates the molecular response to photic stimuli in the SCN.

overall_design: 1) Bulk RNA seq for light stimulation in wildtype mice: 2-4 replicates are involved in each condition. There are two dark control conditions, one is from CT17, the beginning of the light pulse and the other is from CT23, the end of the light pulse. In addition, there are 4 light pulse conditions, 0.5, 1, 3, and 6 hrs in length of light simulation. Each replicate contains 6 pairs of SCNs. 2) Bulk RNA seq for light stimulation in Npas4 null mice and control wild type littermates: 3 replicates are involved in each condition. There are 4 conditions total: wildtype with and without 1 hr light pulse at CT17 and Npas4-/- mice with and without 1 hr light pulse at CT17. Each replicate contains 6 pairs of SCNs. 3) ChIPseq: Two samples, each containing 2 pairs of SCN collected with or without 1 hr light stimulation. 4) Single nuclei sequencing: In total, 10 samples were analyzed. The first batch contains one dark control and one 1 hr light stimulation condition and sequencing was done by Illumina Hiseq. The second batch contains four dark control replicates and four 1 hr light stimulation replicates and sequencing was performed twice by Illumina NovaSeq.

first: Stefano

last: Berto

first: Ashwinikumar

last: Kulkarni

first: Pin

last: Xu

first: Joseph

last: Takahashi


title: Single-cell RNA sequencing of human giant cell tumor of bone

city: Nanning

first: Wenyu

last: Feng

state: Guangxi

address: Shuangyong road 22

department: Center for Genomic and Personalized Medicine

institute: Guangxi Medical University

summary: We performed the scRNA-seq analysis of 1 giant cell tumor of bone tissues based on the 10X Genomics platform and obtained data of 11385 cells.

overall_design: Primary giant cell tumor of bone tissues from 1 patient were used for single cell RNA sequencing by 10X Genomics

first: Mingwei

last: He

first: Yun

first: Qingjun

last: Wei


title: RqcH and RqcP catalyze processive poly-alanine synthesis

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

institute: Universitaet Hamburg

summary: In the cell, stalled ribosomes are rescued through ribosome-associated protein quality-control (RQC) pathways. We demonstrate that RqcH is responsible for tRNAAla selection during RQC elongation, whereas RqcP lacks any tRNA specificity. The ribosomal protein uL11 is crucial for RqcH, but not RqcP, recruitment to the 50S subunit, and B. subtilis lacking uL11 are RQC-deficient. Through mutational mapping, we identify critical residues within RqcH and RqcP that are important for interaction with the P-site tRNA and/or the 50S subunit. Collectively, our findings provide mechanistic insight into the role of RqcH and RqcP in the bacterial RQC pathway. the synthesis of C-terminal poly-Alanine ‘tail’. While it is well-established that RqcP and RqcH are essential for poly-Alanine-tailing in living cells, here, by reconstituting the RQC elongation biochemically we provide a direct proof that the two factors are sufficient. We demonstrate that while RqcH is responsible for tRNAAla selection during RQC elongation, RqcP lacks the tRNA specificity. Through mutational mapping we show that stable interaction of RqcP with 23S rRNA – but not with tRNA – is crucial for RQC, supporting the role of the E-site bound RqcP as a pawl of RQC elongation ratchet. We show that ribosomal protein uL11 is crucial for RqcH – but nor RqcP – recruitment to 50S, and B. subtilis lacking uL11 is RQC-deficient. Finally, we show that proteins encoded by non-stop mRNAs are not universally efficiently targeted by RQC, and that simultaneous disruption of RQC and trans-translation results in bacterial filamentation

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: B. subtilis cell lysate and RqcH-bound (i.e. immunopreciptated, RqcH-IP) tRNAs used for tRNA microarrays to measure tRNA abundance - 4 biological replicates in total; 3 - RqcH-IP and 1 - total tRNA (lysate)

first: Christine

last: Polte

first: Hiraku

last: Takada

first: Caillan

last: Crowe-McAuliffe

first: Vasili

last: Hauryliuk

first: Daniel

last: Wilson


title: Anti-PD-L1 Lead-in Before MAPKi Combination Maximizes Anti-Tumor Efficacy and Immunity [scRNAseq and scTCR-seq]

city: LOS ANGELES

first: Sixue

last: Liu

state: California

address: 10833 Le Conte Avenue

department: Medicine

institute: UCLA

summary: Indications of PD-1/L1- and MAPK-targeted therapies cross cancer histologies. Rationally sequencing and/or combining them may overcome innate and acquired resistance. We observed increased clinical benefit of BRAF andV600MUT/MEK inhibitors in patients with advanced BRAFV600MUT melanoma who were previously treated with immune checkpoint therapy (ICT). To test whether ICT primes MAPK inhibitor (MAPKi) efficacy, we compared sequential/combinatorial regimens in subcutaneous mouse tumors driven by BrafV600, Nras, Nf1 or Kras mutations. The most efficacious regimen consisted of anti-PD-L1 lead-in preceding MAPKi combination and specifically promoted intratumoral pro-inflammatory macrophages and clonal expansion of IFNhi, CD8+ cytotoxic T-cells (relative to CD4+ regulatory T-cells) that highly expressed activation and cytolytic genes. Since melanoma brain metastasis (MBM) and its propensity for therapeutic resistance limit patient survival, we developed an experimental metastasis model of BrafV600MUT MBM. Sequencing anti-PD-L1 before MAPKi combination resulted in superior MBM control and survival as well as robust intratumoral T-cell clonal expansion both intracranially and extracranially. We propose that brief anti-PD-1/L1 dosing prior to MAPKi co-treatment suppresses resistance.

overall_design: This dataset contains the scRNAseq and scTCR-seq data of intratumoral CD45+ cells in murine melanoma model  (Nf1 mutated) under different treatment conditions

first: Yujue

last: Wang

first: Alain

last: Algazi

first: Shirley

middle: H

last: Lomeli

first: Zhentao

last: Yang

first: Yan

first: Megan

last: Othus

first: Xiaoyan

first: Chris

middle: E

last: Randolph

first: Stephanie

middle: D

last: Byrum

first: Alan

middle: J

last: Tackett

first: Antoni

last: Ribas

first: Marco

last: Piva

first: Gatien

last: Moriceau

first: Roger

middle: S

last: Lo


title: MicroRNA expression profiling of livers from the conditional doxycyline-regulatable c-Myc-driven liver tumor mouse model during tumor development and regression.

city: Hannover

first: Asha

last: Balakrishnan

state: Lower saxony

address: carl neuberg str. 1

department: Gastroenterology, Hepatology, and Endocrinology

institute: Hannover Medical School (MHH)

summary: Progressing and regressing liver tumor tissues (depending on the group) were subjected to miRNA profiling to identify the miRNA changes occuring during tumor development and regression. Conditional doxycyline-regulatable c-Myc-driven mice get liver tumors following doxycycline (Dox) withdrawal from their diet. When mice are re-administered Dox through their diet, tumors start to regress.

platform_organism:
Mus musculus
Murid betaherpesvirus 1
Murid gammaherpesvirus 4

overall_design: In this study, the developing tumor group (ULST) and the regressing tumor group 'treated' (re-administrered through food) with doxycycline (TLST), each group had four mice per group, ie., biological replicates (1-4).


title: Single cell atlas of the mouse foetal liver

status: Public on Aug 18 2021

city: milano

first: Saverio

last: Minucci

address: via Adamello 16

institute: European Institute of Oncology

summary: To dissect the early aspects of liver haematopoiesis as well as the development of other liver cell lineages we generated a new single cell RNA-seq (scRNA-seq) atlas of the mouse E12.5 liver

overall_design: 2 single cell suspensions from total E12.5 liver were rapidly obtained and purified before single cell cDNA libraries were independently prepared and sequenced

first: Elena

last: Ceccacci

first: Emanuela

last: Villa

first: Christiana

last: Ruhrberg

first: Alessandro

last: Fantin


title: Anti-PD-L1 Lead-in Before MAPKi Combination Maximizes Anti-Tumor Efficacy and Immunity.

first: Sixue

last: Liu


title: Anti-PD-L1 Lead-in Before MAPKi Combination Maximizes Anti-Tumor Efficacy and Immunity [TCRseq]

overall_design: This dataset contains the TCR-seq of brian and ovary metastases in murine melanoma model  (Braf mutated) under different treatment conditions

first: Yujue

last: Wang

first: Alain

last: Algazi

first: Shirley

last: Lomeli

first: Zhentao

first: Yan


title: Loss of N1-Methylation of G37 in tRNA Induces  Ribosome Stalling and Reprograms Gene Expression

city: Baltimore

first: Allen

last: Buskirk

state: MD

address: 725 N. Wolfe St

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

summary: N1-methylation of G37 is required for a subset of tRNAs to maintain the translational reading-frame. While loss of m1G37 increases ribosomal +1 frameshifting, whether it incurs additional translational defects is unknown. Here we address this question by applying ribosome profiling to gain a genome-wide view of the effects of m1G37 deficiency on protein synthesis. Using E. coli as a model, we show that m1G37 deficiency induces ribosome stalling at codons that are normally translated by m1G37-containing tRNAs. Stalling occurs during decoding of affected codons at the ribosomal A site, indicating a distinct mechanism than that of +1 frameshifting, which occurs after the affected codons leave the A site. Enzyme- and cell-based assays show that m1G37 deficiency reduces tRNA aminoacylation and in some cases peptide-bond formation. We observe changes of gene expression in m1G37 deficiency similar to those in the stringent response that is typically induced by deficiency of amino acids. This work demonstrates a previously unrecognized function of m1G37 that emphasizes its role throughout the entire elongation cycle of protein synthesis, providing new insight into its essentiality for bacterial growth and survival.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Ribosome profiling and RNA-seq E. coli cells to study the effects of loss of the tRNA methylase TrmD either by 1) a degron strategy using ClpXP or 2) a knockout strain where Trm5 is expressed initially and then repressed


title: miRNA profiling in URSA patients and control subjects

city: Jinan

first: Xiaoxiao

last: Zhu

address: 18877 Jingshi Road

institute: Shandong First Medical University & Shandong Academy of Medical Sciences

summary: A total of 39 miRNAs were either up- or down- regulated by at least 1.5-fold and P value< 0.05 in the RSA, including 20 up-regulated miRNAs and 19 down-regulated miRNAs

overall_design: Total RNA was extracted from PBMCs using TRIzol (Invitrogen, Carlsbad, CA, USA). The genome-wide analysis of miRNA expression in URSA patients (n= 3) and normal pregnancy subjects (n= 3) were performed using Human miRNA, Release 21.0 (8*60K, Design ID:070156).

first: Chu

last: Chu

first: Bin

first: Wen

first: Xia

last: Li


title: The novel long noncoding RNA lncRNA-AU021063, induced by IL-6/Arid5a signaling, exacerbates breast cancer invasion and metastasis by stabilizing Trib3 and activating the Mek/Erk pathway (mRNA-Seq)

first: Daisuke

last: Okuzaki

overall_design: We performed RNA-sequencing analysis using samples of WT and shAU021063-4T1 cells duplicate.

first: Kishan

middle: K

last: Nyati

first: Tadamitsu

last: Kishimoto


title: Gene expression profile of Sca-1+ versus Sca-1- endothelial cells selected from the bone marrow of normal B6 mice

city: Pasadena

first: David

middle: Eugene

last: Frankhouser

address: 1500 E Duarte Rd

department: Population Sciences

institute: City of Hope

summary: Different gene expression profile was observed in bone marrow Sca-1+ versus Sca-1- endothelial cells

overall_design: CD45-Ter119-CD31+Sca-1+ (Sca-1+) and CD45-Ter119-CD31+Sca-1- (Sca-1-) endothelial cells from the bone marrow of normal wild-type mice were sorted by flow cytometry and used for RNA-seq.

last: Zhang


title: Comprehensive analysis of the expression profiles of lncRNAs in a mouse model of alcoholic liver disease

city: Hangzhou

first: Wenwen

last: Yang

address: No.548 Binwen Road, Binjiang District

department: School of Life Science

institute: Zhejiang Chinese Medical University

summary: Background and Aim: The worldwide prevalence of alcoholic liver disease (ALD) due to escalating alcohol consumption has presented an unprecedented pressure on human health. A few studies have determined long non-coding RNAs (lncRNAs) involved in the pathogenesis of liver diseases. However, the roles of lncRNAs in ALD development is still poorly understood. Methods: An ALD mouse model was established and confirmed. Expression profiles of lncRNAs were obtained by whole transcriptome sequencing. The altered lncRNAs in ALD mice were further verified by qRT-PCR. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used to enrich the functions of these lncRNAs. In combination with miRNA and mRNA profiles, we constructed concise endogenous RNA (ceRNA) networks. The function of the most up/downregulated lnRNA signaling was further verified and investigated in both ALD model and AML-12 cells. Results: Totally, five downregulated lncRNAs were obtained and verified in ALD mice. The GO term and KEGG pathway analyses revealed that the identified lncRNAs were associated with alcohol-induced hepatic oxidative damage, cellular inflammation, and lipid metabolism. Integration the differentially modulated miRNAs and mRNAs with ceRNA network analysis, we constructed five ceRNA networks and screened out 30 miRNAs and 25 mRNAs that may participate in ALD. Further, we verified and investigate the function of the most downregulated lnc_1700023H06Rik. Depletion lnc_1700023H06Rik reduced genes related to lipid metabolism, especially mRNA Acat2 (ENSMUST00000159697) and Pgrmc2 (ENSMUST00000058578) in both ALD mice and AML12 cell. Knocking down lnc_1700023H06Rik induced triglyceride accumulation and LDH leakage in AML12 cells, consisting with that in alcohol-treated cells, confirming the potential pathological role of lnc_1700023H06Rik in ALD. Conclusion: The five remarkably downregulated lncRNAs in an ALD mouse model were identified as novel biomarkers, highlighting the key role of lncRNAs in the development of ALD. The effect of lnc_1700023H06Rik was further verified.

overall_design: hepatic miRNARNA profiles of 8-weeks old pair-fed (PF) and alcohol-fed (AF) mice

first: Xiaobing

last: Dou

first: Songtao


title: Myometrial transcriptional signatures at spontaneous human term labor (TL) and at term not in labor (TNL)

first: Chaolu

last: Chen

address: Xueshi Road

institute: Women’s Hospital, School of Medicine, Zhejiang University

summary: The study evaluated the differences in the transcriptomic in myometrium from women in spontaneous labor and not in labor, both at term.

overall_design: Transcriptional signatures of myometrium from women at spontaneous term labor (TL) and term not in labor (TNL).

first: Shuaiying

first: Danqing


title: Gene expression profile of exposed human salivary gland cells line to MeHg

city: Belém

first: Lygia

middle: Sega

last: Nogueira

state: PA

address: R. Augusto Correa 01

institute: Federal University of Pará

summary: The goal of the study was perform the transcriptome profile of the human salivary gland cell line after exposure to MeHg for 24h using the microarray technique and posterior bioinformatics analysis.

overall_design: The MeHg exposure did not cause lethality in the human salivary gland cells line but was able to change the expression of 155 genes.

first: Rafael

last: Lima


title: Integration of RNA-Seq and ATAC-Seq Identifies Key Genes and chromatin accessibility changes in Growth hormone-secreting pituitary adenoma

first: Xuelong

last: Wang

address: No. 100 Banxia Road

institute: Chinese Academy of Sciences

summary: Background: Growth hormone-secreting pituitary adenoma (GHPA) is an insidious disease with persistent hypersecretion of growth hormone and insulin-like growth factor 1, leading to increased morbidity and mortality. Though treatments for GHPA have greatly improved, lack of deep knowledge on the precise molecular mechanisms involved in GHPA hinders the development of therapeutic approaches. Few studies have attempted to reveal the genome-wide landscape of GHPA. As chromatin structure change exerts significant influence on gene transcription, herein, we investigated the landscape of chromatin accessibility. Methods: Both assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and RNA sequencing (RNA-seq) were applied to identify the differential expression genes (DEGs) and uncover chromatin accessibility changes and the potentially associated transcription factor (TFs) in somatotropinoma tissues. Results: 64 DEGs were obtained, including 10 DEGs were elevated in the tumors and 54 DEGs were negligibly expressed in adenomas. A total of 3916 increased and 2895 decreased chromatin-accessible regions were identified nearby these DEGs. The majority of DEGs associated with closed chromatin regions were significantly down-regulated in our study, while the most of DEGs near open chromatin were not expectantly up-regulated. Additionally, the newly opened and closed chromatin regions were highly enriched for GRE and CTCF transcription factor binding sites, which were potentially relevant to the regulation of chromatin accessibility and genes expression in GHPA. Conclusion: Collectively, our results reveal the landscape of chromatin accessibility and unique enhancer in GHPA, which may, at least in part, contribute to tumorigenesis and provide a new field of drug development.

overall_design: Examination of different chromatin accessibility and gene expression in growth hormone-secreting pituitary adenoma tissues compared to para-adenoma normal tissues

first: Zhao

last: Ye


title: A chromatin immunoprecipitation database for prokarytic organisms [RpoD]

city: La Jolla

first: Ye

last: Gao

address: 9500 Gilman Dr.

institute: UCSD

summary: Bacterial transcription factors (TFs) regulate gene expression to adapt to changing environments; when combined, the TF’s regulatory actions comprise transcriptional regulatory networks (TRNs). The chromatin immunoprecipitation (ChIP) assay is the major contemporary method for mapping in vivo protein-DNA interactions in the genome. It enables the genome-wide study of transcription factor binding sites (TFBSs) and gene regulation. Although rapidly accumulating publicly-available ChIP data are a valuable resource for the study of gene regulation, there are no full datasets of key regulators in E. coli K-12 MG1655. Here, we present the genome-wide binding for major TFs in the E. coli K-12 MG1655.

overall_design: Identification of genome-wide bindings for sigma factors in E. coli K-12 MG1655, using ChIP-exo technology

first: Bernhard

last: Palsson


title: Identification of differentially expressed genes using microarray analysis and COL6A1 induction of bone metastasis in non-small cell lung cancer

city: Shijiazhuang

first: Zong

middle: mao

last: Zhao

address: 215 West Heping Road

institute: The Second Hospital of Hebei Medical University

summary: Non-small cell lung cancer (NSCLC) is a major cause of cancer-associated mortality worldwide, and bone metastasis is the most prevalent event observed in patients with advanced NSCLC. However, the pathogenesis of bone metastases has not been fully elucidated. In the present study, differentially expressed genes (DEGs) were identified by gene expression microarray analysis of NSCLC tissue samples with or without bone metastases. Subsequently, collagen family collagen 6A1 (COL6A1) was chosen as the target gene through Ingenuity Pathway Analysis and reverse transcription-quantitative (RT-q)PCR validation of the top eight DEGs. COL6A1 was overexpressed or knocked down, and the proliferation and invasion of NSCLC cells was assessed using Cell Counting Kit-8, colony formation and Transwell invasion assays. Additionally, the osteogenic capacity of HOB and hES-MP 002.5 cells was assessed using RT-qPCR, western blotting, Alizarin Red staining and alkaline phosphatase staining. A total of 364 DEGs were identified in NSCLC tissues with bone metastases compared with NSCLC tissues without bone metastases, including 140 upregulated genes and 224 downregulated genes. Gene Ontology analysis indicated that the upregulated and downregulated genes were primarily enriched in ‘cellular process’, ‘metabolic process’ and ‘biological regulation’. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed that the upregulated genes were primarily enriched in ‘cysteine and methionine metabolism’, ‘oxidative phosphorylation’ and the ‘ribosome’, while the downregulated genes were primarily enriched in ‘transcriptional mis-regulation in cancer’, ‘ribosome’ and ‘mitophagy in animals’. COL6A1 was highly expressed in NSCLC tissue samples with bone metastases. Functionally, COL6A1 overexpression induced the proliferation and invasion of HARA cells, and knockdown prevented the proliferation and invasion of HARA-B4 cells. Finally, it was demonstrated that HOB and hES-MP 002.5 cells exhibited osteogenic capacity, and overexpression of COL6A1 in HARA cells increased adhesion of these cells to the osteoblasts, whereas knockdown of COL6A1 in HARA-B4 cells reduced their adhesive ability. In conclusion, COL6A1 may serve as a potential diagnostic marker and therapeutic target for bone metastasis in NSCLC.

first: Zongmao


title: Examination of HMGA2 binding genes in human HMGA2-exogenous overexpressed gastric cancer cells

city: Hohhot

first: zhouying

last: Wu

state: Inner Mongolia Autonomous Region

address: No. 20 Zhaowuda Road, Saihan District

department: Clinical Medical Research Center

institute: Inner Mongolia People’s Hospital

summary: HMGA2 significantly increased cell proliferation capacity of gastric cancer in a HMGA2-dependent manner both in vivo and in vitro and we found HMGA2 promoted GC through accelerating S-G2/M phase.To elucidate the underlining mechanism by which HMGA2 induced the change of phenotype in GC cells, we performed ChIP-seq analysis of HMGA2-OE MKN-45 cells with anti-HMGA2 antibody.

overall_design: Next Generation Sequencing of  HMGA2 bound genomic DNA in human HMGA2-exogenous overexpressed gastric cancer cells

first: Lan

last: Yu

first: Zhouying

first: Min

first: Feng


title: RNA sequencing of fibroblasts with or without CSMD1 knockdown

first: Shuchen

last: Gu

institute: Shanghai Ninth People's Hospital

summary: CSMD1 gene, mapping to human chromosomal region 8p23, encodes a transmembrane protein with an extracellular region containing 14 CUB and 28 sushi domains, a transmembrane domain and a cytoplasmic domain with a putative tyrosine phosphorylation site.The loss of CSMD1 has been found to be associated with enhanced cell proliferation, migration and poor prognosis in head and neck squamous cell carcinoma (HNSCCs), lung squamous cell carcinoma (SCCs), melanoma, and breast cancer, suggesting its role as a tumor suppresser.However, its role in hypertrophic scar has not been uncovered. So we decided using fibroblasts to see its transcriptomes changing after CSMD1 knockdown.

overall_design: Examination of fibroblasts RNA sequencing comparing the CSMD1 knockdown group and control group

first: Xin

last: Huang

first: Tao

last: Zan


first: Wenwen

country: Zimbabwe

overall_design: hepatic lncRNA profiles of 8-weeks old pair-fed (PF) and alcohol-fed (AF) mice

first: Xiaobing

first: Songtao

last: Li


title: Micro-engineered perfusable 3D-bioprinted glioblastoma model for in-vivo mimicry of tumor microenvironment

city: Tel Aviv

first: Ronit

last: Satchi-Fainaro

address: Klatzkin 35

department: physiology and pharmacology

country: Israel

institute: Tel Aviv University

summary: We aimed to evaluated the effect of the cells growth conditions on the genetic profile of the cells. More specifically, we wanted to evaluate whether our 3D cancer model better reflects the in vivo scenario than 2D culture methods . Therfore, we performed RNA-seq of glioblastoma tumors grown in mice and compared it to a "penta-culture" comprised of GL261 murine GB cells, primary astrocytes, microglia, pericytes, and endothelial cells, grown in 2D or in 3D-bioink

overall_design: Comparisom of gene expression between GL261 glioblastoma cells grown in mice to GL261 cells grown togather with the brain microenvironment cells (murine primary astrocytes, microglia, pericytes and endothelial cells)  in 2D culture or in fibrin 3D-bioink. Bulk RNA.

first: Asaf

last: Madi

first: Lena

last: Neufeld

first: Eilam

last: Yeini


title: Genomic and transcriptomic analysis of Bovine P.multocida serogroup A strains reveals insights into virulence attenuation

city: ChangChun

first: JiaQi

last: Zhang

address: XinCheng Street

institute: Jilin Agricultural University

summary: Pasteurella multocida is one of the main pathogens of bovine respiratory disease (BRD), which has brought great losses to the cattle industry. The Pm3 strain was a natural isolates, its pathogenic stronger and sensitive to fluoroquinolones. A highly fluoroquinolone resistant strain Pm64(MIC=64 μg/mL) was formed after continuous induction with subinhibitory concentration (1/2MIC) of enrofloxacin，with the enhanced growth characteristics and large attenuation of pathogenicity in mice. In this study, we report the whole genome sequence and the transcription profile by RNA-Seq of strain Pm3/Pm64. The results showed that there was not too much difference between the two strains at the genome level, 24 and 8 genes could be recognized were added and lost in the gene islands(GIs) of Pm64, Those gene involved in DNA binding, trehalose metabolism, material transportation, capsule synthesis, prophage, amino acid metabolism and other functions. 558 up-regulated and 568 down-regulated genes were found in Pm3 campared with Pm64, from which 20 virulence factor-related DEGs were screened. Genes differentially transcribed were mostly associated with capsular polysaccharide(CPS), lipopolysaccharide (LPS), lipooligosaccharide (LOS), Iron utilization and biofilm composition. We speculated that the main mechanism of virulence attenuation after the formation of resistance of Pm64 comes from the change of the expression profile of these genes. This report helps to elucidate the toxicity targets of P. multocida serogroup A and provide helps for the following research on pathogenesis and antimicrobial drugs development.

first: Zhang

last: Jiaqi


title: Transcriptome profiling of left ventricles from cardiac-specific miR-150 conditional knockout mice

city: Indianapolis

first: Il-Man

last: Kim

state: IN

address: 635 Barnhill Drive, MS 346A

institute: INDIANA UNIVERSITY SCHOOL OF MEDICINE

summary: Genome-wide transcriptomic analyses in left ventricles (LVs) from cardiac-specific miR-150 conditional knockout KO (cKO) mice were performed to identify novel miR-150 targets in the heart.

overall_design: The following 12 independent mouse LVs were used: three biological replicates for 4 groups (sham miR-150 floxed/floxed [miR-150 fl/fl], sham alpha-MHC-Cre;miR-150 fl/fl [miR-150 cKO], myocardial infarction [MI] miR-150 fl/fl and MI miR-150 cKO). LVs were harvested after 4 weeks of sham or MI surgeries.

first: Tatsuya

last: Aonuma


title: Human Placental Transcriptome and fetal sex differences in Spontaneous Preterm Birth

city: Philadelphia

first: Zhe

address: Translational Research Lab

institute: University of Pennsylvania

summary: Placental insufficiency is implicated in spontaneous preterm birth (SPTB). We performed RNA-seq study in male and female placentas from women (African American, self-identified) with SPTB (< 36 weeks gestation) compared to normal pregnancies (≥ 38 weeks gestation) to assess the alterations in gene expression profiles.

overall_design: Examination of transcriptomes in 4 experimental conditions (SPTB males, SPTB females, Term males, and Term females)

first: Yu-Chin

last: Lien

first: Rebecca

middle: A

last: Simmons

first: Yi

last: Cheng

first: Erzsebet

last: Polyak

first: Marni

last: Falk

first: Michal

last: Elovitz

first: Samuel

last: Parry


title: Expression data from Sarcoma Tumors expressing the EWSR1-CREB fusions

city: New York

first: Fabio

last: Vanoli

state: NY

address: 1250 1st Avenue

institute: MSKCC

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Expression data from Sarcoma Tumors expressing the EWSR1-CREB fusions [microarray]

summary: Sarcoma is a rare form of tumor characterized by the presence of oncogenic fusion, that is often the only aberration identified. U133A Affymetrix arrays were used to identify the expression signature of 3 different types of sarcoma: AFH, CCS and GI-CCS harboring the EWSR1-CREB1 and EWSR1-ATF1 chromosomal translocation.

overall_design: Expression profiling of two types of sarcoma: Angiomatoid Fibrous Histiocytoma (AFH) and Clear Cell Sarcoma (GI-CCS)

first: Cristina

last: Antonescu


title: FOXM1-AKT positive regulation loop provides venetoclax resistance in AML

city: Chicago

first: Leonid

last: Feferman

state: Illinois

address: 1737 West Polk St

department: Research Resources Center

institute: University of Illinois at Chicago

summary: FOXM1 and AKT are crucial pro-oncogenic regulators of cancer therapy resistance. Due to reciprocal regulatory links they establish a positive feedback autoregulation loop in AML cells. Disruption of this loop via inhibition of either FOXM1 or AKT results in similar gene expression changes, drastic upregulation of HOXA genes and sensitization of AML cells to cytarabine and venetoclax treatment.

overall_design: For each experimental model and condition, two biological replicates were analyzed. Control samples were treated with viehicle alone (DMSO), with vehicle percentage not exceeding 0.3%.

first: Mikhail

last: Chesnokov

first: Soheila

last: Borhani

first: Marianna

last: Halasi

first: Zarema

last: Arbieva

first: Irum

last: Khan

first: Andrei

middle: L

last: Gartel


title: XPO1/CRM1 is a promising prognostic indicator for neuroblastoma and represented a therapeutic target by selective inhibitor KPT-335.

city: Shanghai

first: Lijia

last: Pan

address: Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, 1665 Kongjiang Road, Shanghai, 200092, China.

summary: The five-year survival rate remains less than 50% for high-risk neuroblastoma patients, few of them show effective response to current chemotherapy drugs. It is urgent to identify new therapeutic targets and corresponding drugs for high-risk neuroblastoma. Exportin-1(XPO1), also known as chromosomal region maintenance 1 (CRM1), plays important roles in the progress of tumorigenesis. However, the prognostic and therapeutic values of XPO1 in neuroblastoma have not been reported. Here, our results showed that overexpression of XPO1 was significantly associated with poor clinical characteristics and prognosis of neuroblastoma patients. The specific inhibitor of XPO1 suppressed neuroblastoma cell growth both in vitro and in vivo. Specifically, inhibition of XPO1 suppressed neuroblastoma cells proliferation and induced cell apoptosis by FOXO1 and RB1 nuclear accumulation in neuroblastoma through inhibiting PI3K/AKT pathway, and induced G0/G1 phase cell arrest by activating P53 function. Together, XPO1 is a promising prognostic indicator for neuroblastoma and a novel target for antitumor treatment by selective inhibitor verdinexor (KPT-335).

overall_design: SK-N-BE(2) mRNA profiles of DMSO treatment and KPT-335 treatment

first: Cheng

first: Peiwen

last: Duan

first: Kai

last: Chen

first: Yeming

last: Wu

first: Zhixiang